Combined aircraft hybrid fuel cell auxiliary power unit and environmental control system and methods are disclosed. In one embodiment, an auxiliary power unit includes a fuel cell component which chemically converts combustible fuel into electrical energy. Unutilized fuel emitted by the fuel cell component is combusted by a burner to generate heated gas. The heated gas is received by and drives a turbine, which in turn drives a drive shaft. A compressor, coupled to the drive shaft, compresses a source of oxidizing gas for supplying compressed oxidizing gas to the fuel cell component and to an environmental control system. A heat exchanger controls the temperature of the pressurized air leaving the environmental control system to provide the cabin air supply. Finally, a generator is coupled to the drive shaft to be driven by the turbines to generate additional electrical energy.